


The Shadows in the Light

by alifish1988



Category: Mass Effect
Genre: Anal Fingering, Anal Sex, Angst, F/F, F/M, Fluff, M/M, Mention of attempted suicide, lots and lots of angst
Language: English
Status: In-Progress
Published: 2016-07-20
Updated: 2017-02-19
Packaged: 2018-07-25 14:41:40
Rating: Explicit
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 6
Words: 7,989
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/7536772
Author URL: https://archiveofourown.org/users/alifish1988/pseuds/alifish1988
Summary: <blockquote class="userstuff">
              <p>Two years ago the reapers were destroyed and Kaidan was left with nothing. Now something is stirring in the shadows.</p>
            </blockquote>





	1. Prologue

Kaidan yells out when he moves a large piece of rubble causing more to rain down, thankfully it was only small pieces. For two days now they have been searching the citadel for Shepard, with the three days to get here on top of that, Kaidan is starting to lose hope. He moves another large rock revealing a body.

"I found Anderson, he's gone." Kaidan calls out after checking for a pulse. "Shepard shouldn't be too far away."

"I got the Illusive man over here." Garrus hollers then looks closer at the gunshot in his head. "Perfect shot between the eyes, nice one Shepard."

Kaidan looks around ignoring the chatter starting up behind him, he sees a pile of rubble with what looks like a hand reaching out. He hurries over and begins moving rocks and metal beams until he reveals a burnt and mangled body completely unrecognizable. With shaking fingers Kaidan grabs the dog tags and looks at the name.

"SHEPARD!" Kaidan cries out throwing himself on Shepards body.

The rest of the crew rush over. "Goddess no." Liara sobs out turning to Javik for comfort who looks shaken as well.

Dr. Chakwas comes over and places her hand on Kaidan's shoulder. "I'm sorry Kaidan we need to move the body and confirm the ID." She says

"Confirm the ID. These are his tags!" Kaidan yells ripping the dog tags off the body. "He's gone." 

Kaidan turns around and runs hoping if he can run fast enough it might not hurt so much. Tears blur his vision making it impossible to see. Kaidan trips and falls but doesn't get up, he can feel a migraine coming on and hopes that maybe this one will kill him so he can be with Shepard again. Before long Garrus and Liara find him curled up in agony, they help him back to the shuttle. He is brought to Dr. Chakwas who sets him in a bed and applies a sedative. 

When Kaidan wakes up he quietly leaves the med bay ignoring the blanket covered bed hiding Shepards body, he only stops to grab Shepards dog tags. He makes his way to their cabin where he gathers up his few belongings. He stares at Shepards N7 hoodie before gently folding and putting it in his bag as well as a picture of them together and the SR-1 model, Shepards favourite. Hefting his duffle on his shoulder Kaidan leaves the Normandy and takes a shuttle to Vancouver, only planning on returning for Shepards funeral. 

***

Jordan takes a final look over his report before sending it to headquarters, he deactivates his omni-tool then leans back in his chair. He rests for a moment before getting up and going to the comm room to report to Mr. Manning. At least he has good news this time, he had nothing to report last time and that is something he definitely does not want to repeat. Sighing he activates the comm, the image of a middle aged man in an expensive suit appears. 

"Operative Bernfield. I have received your report, everything seems to be going well. I expect the imperium protocol to begin immediately." Mr. Manning says.

"Sir, I would recommend waiting until regeneration is complete." Jordan says cautiously.

"No, control is essential we will not make the same mistake as my predecessor." Mr. Manning replies sternly.

"As you wish sir." Jordan says with a salute.

"I will expect a report in a month. Do not disappoint me." Mr. Manning says then disconnects the comm.

Grinding his teeth slightly Jordan connects to his crew. "Begin the imperium protocol." He says.

"But sir, it's too soon we could lose the subject." A women voice replies.

"I know Grace... Just do it, we will monitor his vitals and slow things down if he starts having problems." Jordan says. 

Jordan hurries to his office and drops down in his chair. He uses his computer to send a few orders then brings up a live feed. A man burned and broken beyond belief lays on a table, countless tubes pump colourful fluids into him while other machinery moves around repairing the damaged body. Jordan's not a religious man but it's a miracle they found him alive, something was helping him hold on. Hopefully he will survive everything they have planned.


	2. Remembering A Hero

Kaidan stands in the shower watching the water drip down his chest, trickling between the two sets of dog tags, his own and Shepards. He grips them in his hand gently tracing the ragged lettering of Shepards name with his thumb, hoping to draw some much needed strength. It's been two years since he found Shepard but the pain is still fresh. Letting out a sigh he shuts off the shower and towels himself dry before dressing in black pants and a dark blue dress shirt. Kaidan looks at himself in the mirror while brushing his hair out, he straightens a few imagined wrinkles on his shirt then silently leaves his apartment grabbing his jacket along the way. It's the annual get together of the Normandy crew, they are going to meet at a small bar a few blocks from his place.

Kaidan does up his jacket then sets out to the bar, deciding to walk since it is so close and he is planning on getting extremely drunk. He shoves his hands into his pockets and starts making his way to the bar. It only takes a few short minutes to get there, when he enters the bar he is waved over by James and Steve who have pushed several tables together so the whole crew can sit together. Kaidan sits down and orders a beer and a shot of whiskey when the waitress comes over. Soon the rest of the crew start filing in, Liara sits down beside Kaidan and smiles at him before ordering a drink.

"Hey Kaidan. How are you doing?" Liara asks.

"Yeah we heard you've been busy this year Blue." James remarks.

"I'm good. Been picking up more spectre missions... I've been thinking about leaving the biotics division." Kaidan says.

"You might as well, I've been covering your ass for months now." Jack says while taking a seat.

"I know, it just... It leaves me with too much time to think, I'm better out there getting my hands dirty." Kaidan says sadly remembering another time he said almost the same thing.

Liara puts her hand on his shoulder trying to comfort him, he reaches up and takes her hand with his appreciative of the gesture. Him and Liara got close right after Shepard died, he was in a dark place then and if it wasn't for Liara he wouldn't be here right now. Kaidan downs his shot then takes a drag from his beer. By the time everyone has arrived Kaidan has had another shot and finished his first beer. After everyone has settled down Steve and James stand up their hands clasped together.

"We have an announcement." Steve says with a smile.

"Yeah me and Esteban are getting married." James says his excitement thick in his voice.

Kaidans heart lurches at the mention of marriage but he ignores it and puts on a smile, congratulating them both. He settles back down with his drink as everyone else asks about dates and themes. He is stirred out of his thoughts when he feels Liara's hand on his shoulder again grounding back in reality. Kaidan takes a deep breath helping to clear his mind from unneeded thoughts. He turns his attention back to the group, thankfully the conversation has changed topic.

"So Liara any earth shattering news?" Garrus asks.

"No, things have been surprisingly quiet. It actually has me a little concerned, even the pirates are keeping amazingly low key." Liara replies.

"Well that can't be good. I'll check with my contacts and see if they have heard anything." Miranda says.

"I appreciate it Miranda. I am worried that they are banding together again, hoping to take out a major colony." Liara says.

"Make sure you keep me in the loop. I can get a team together to take care of them if need be." Kaidan pitches in.

"I will." Liara replies.

The rest of the night was spent remembering Shepard and times on the Normandy, it soon becomes a haze as Kaidan gets more and more drunk. When last call is announced Kaidan is throughly smashed and stumbling on his feet. Liara goes to help him home but he gently pushes her away.

"I'm... k Lara. Just aroun corner... be fine." Kaidan slurs out then stumbles his way outside.

He sees her force herself not to follow, respecting his decision, he appreciates that because right now he needs to be alone. It only takes Kaidan a few minutes extra to get back to his apartment. He closes the door then collapses to his knees as his memories take over and tears begin to fall.

_Kaidan pulls Shepard away from the party nervously leading him to the side hall. His heart racing, he turns around patting his pocket assuring that the small box is there._

_"You alright Kaidan?" Shepard asks._

_"John... I know we have only been together for a few months but deep down I have always known that you are exactly the kind of person I have been looking for. You are strong, funny and despite what most people believe a deeply caring man and I want to spend the rest of my life with you." Kaidan says then gets down on one knee and pulls the small box from his pocket, opening it and revealing a simple gold band with a small diamond. "John Shepard will you marry me."_

Kaidan drags himself back up to his feet and trudges slowly to his room. Damn Steve and James for dragging these memories back, but as much as it hurts deep down he is happy for his friends. In his room Kaidan opens the closet, with shaking hands he pulls a box from the top shelf and brings it to his bed. He opens the box and pulls out a picture of John and him, he places it on the bed beside him then carefully pulls out a small ring box.

_John looks at him for a moment, his eyes showing all the love in his heart before a mischievous look takes over. "Yes but on one condition." He says pausing just long enough to up Kaidan's heart rate one more notch. "We don't wait. Anything can happen so let's get married tonight."_

" _Tonight... But how, where." Kaidan begins to say but John puts finger to his lips signalling him to be quiet._

_"I will call Kolyat I'm sure he could find someone to do a simple service right here with all our friends. You just have to say yes." John says._

_Kaidan smiles. "How did my proposal turn into you asking me to say yes." He replies happily. "Yes let's do it."_

_John gets a more serious look on his face. "I want to take your name Kaidan, so after the war maybe I can disappear with you and we can live a normal life." He says quietly._

Kaidan opens the small box and pulls out a gold ring with Always inscribed inside. Crying Kaidan puts on the ring and lays down curling around the picture of John, remembering how happy he was then.

***

Councillor Ardellia Crane enters her apartment hardly looking up from her datapad. Today has been difficult the council is still arguing about moving the citadel, she did manage to get the turian councillor to agree with moving it back to the serpent nebula but the salarians and the asari see it as a waste of resources and instead wish to salvage the ancient space station.

Ardellia looks up and gasps when she sees a man completely cloaked in black step out of the shadows, his face is covered with dark material only two blue eyes look out dull and glazed over.

"Ardellia Crane?" He says his voice cold and void of all emotion.

"Y-yes." She replies shakily while trying to slowly back away to her desk where she has a pistol hidden.

"You have been deemed a risk to humanity's progress and have been scheduled for termination." He says in the same cold voice while drawing a small Japanese style sword from a sheath strapped to his back.

Before a scream could rise past Ardellia's lips the sword slides silently through her chest and back out in one smooth motion, blood bubbles from her mouth as she drops. Her datapad clatters to the ground and her body collapses to the floor a pool of blood forming around her. The dark man couches down and checks her pulse before wiping his sword clean on her clothes. He stands up and activates a comm in his ear.

"Target eliminated. Proceeding to next location." He says then activates a cloaking program and disappears.


	3. The Assassin

Kaidan wakes to the sound of his omni-tool beeping informing him of an important call coming in. Groaning he gets up and answers the call, a quick glance at the clock informs him that it is 6am. 

"Sorry to bother you so early Specter Alenko but the councillor has been found murdered." A young RCMP officer says. 

Kaidan instantly wakes up fully. "Yes, I'll be right there." He replies then ends the call.

Kaidan rushes to the washroom where he quickly showers and grooms himself, then he hurries and pulls on some BDU's before putting on his blue Specter armor. Within half an hour he is on his way to Roulin tower. The same officer meets him at the building doors to guide him to the apartment, being a Specter he already knows where the councillor is staying but he indulges her, on the way she says her name is Vivian Peterson. In the elevator he notices that she keeps looking at him then looking away quickly, he knows it most likely because of his part in the war. They reach the top floor and head to the door with the crime scene tape up that officer Peterson quickly deactivates. 

Kaidan takes a deep breath before opening the door, inside the apartment is exactly the same as when he was here two days ago except that Ardellia is laying on the floor in a pool of blood. He picks up a datapad near her hand but it only has her schedule and information about recent meetings. Kaidan carefully searches the councillors body surprised to not find any marks of resistance, she isn't someone who would go without a fight. He scans the stab wound in her chest and is surprised when it comes up as a Japanese style sword.

"Now that's interesting." He mumbles to himself.

"What is sir?" Officer Peterson asks.

Kaidan looks up at her. "The type of weapon used isn't very common." He says.

Kaidan goes back to the door and runs a diagnostic on the security panel which shows a subtle hack used to override it. He looks closer at the hack, it seems familiar but he can't quite place where he might have seen it before. Kaidan takes one last look at the room but knows he won't find anything, what happened here happened quickly and quietly with very little trace left behind.

"Thank you officer Peterson, I'm done here. If you uncover anything new I need you to forward it to me immediately." Kaidan says then turns to leave.

"Of course Spectre Alenko." Officer Peterson replies while following him out and reactivating the crime scene tape. 

Kaidan gets into his skycar and sets the autopilot to take him to Alliance HQ. "Cerberus." Kaidan angrily mutters slamming his fist down on the dash. The entire crime scene reeked of their sickening touch but how, Shepard destroyed them two years ago. Kaidan's omni-tool beeps with an incoming message from officer Peterson. He opens it revealing two more political figures assassinated in the past week, one shot in the head with a black widow rifle and other killed in a similar manner as the councillor, all three victims promote cooperation with aliens and have the political power to make it happen. Kaidan is now completely convinced that Cerberus is back or an organization like them is rising, he sends a message to Admiral Hackett asking to meet with him about vital information.

"So Alenko you believe that Cerberus is behind these assassinations?" Admiral Hackett asks.

"I do sir, or at least a group with similar beliefs." Kaidan replies.

"This is serious. Step into my office, we need to go over the specifics." Hackett says opening the door to a small office.

Kaidan instinctively scans the room and notices a dark figure uncloaking in the corner. He looks at the intruder whose face is covered but familiar deep blue eyes gaze at him and he notices a flicker of recognition before they glaze over and are turned towards the admiral.

"Steven Hackett you have been deemed a risk to humanity and have been scheduled for termination." The figure says in a monotone while drawing a Japanese sword.

Kaidan pushes the admiral aside just as the figure stabs at where his chest had been. Kaidan brings up his barriers and draws his pistol aiming it on the assassin.

"Drop the weapon and identify yourself." Kaidan instructs.

Kaidan watches the assassin take a step back his arms shaking like he is fighting himself. "I... can't." He chokes out then rushes Kaidan who barely manages to knock the sword aside losing his pistol in the process. 

They back off from each other then Kaidan throws a reave but the assassin dodges it and activates his cloaking completely disappearing. Kaidan looks around the room hoping for some sign of where the assassin is, he hears a slight sound behind him and turns around prepared to throw a stasis field but takes a fist to the face making him see stars. Kaidan steps back shaking his head trying to clear his vision then a second hit to the side of his head makes him drop to his knees struggling to stay conscious. He is flipped over onto his back then the assassin straddles him pinning Kaidans arms down and raises his arm back, an omni-blade appears poised above his heart. Kaidan closes his eyes thinking that at least he will be with John, he prepares for the feel of the blade cutting through his chest taking his life but it never comes. He opens his eyes and looks at the assassin who has paused with his arm drawn back and shaking like he is forcing himself to stop, Hackett comes up behind him and bashes him in the head with Kaidans pistol knocking the assassin unconscious.

Hackett aims the gun at the unconscious man then holds out a hand to help Kaidan to his feet. Kaidan goes and rolls the man onto his back then grabs his mask. Time stops as Kaidan removes the mask revealing the face of his dead husband. Shock threatens to take over but Kaidan pushes it down and replaces it with anger, he throws the mask down and walks towards the window.

"It must be a clone." Kaidan says coldly.

Hackett puts the mask back on then sends a message on his omni-tool. Two soldiers show up and pick up the assailant. "Take him to the brig and do not remove the mask." Hackett orders. The soldiers salute then carry the prisoner down to the brig.

Hackett goes over to Kaidan and puts his hand on his shoulder drawing him from his thoughts. Kaidan takes a deep breath and turns to face the Admiral. 

"This proves that Cerberus is on the rise, they cloned Shepard before, I'm sure they could do it again." Kaidan says but can't help thinking about how he didn't, no couldn't kill him. "We need to do some tests then interrogate him."

"We will but you need to go and calm down first." Hackett replies.

"I am calm." Kaidan snaps.

"No you're not. You just saw a ghost." Hackett says calmly. "Go home, I will contact you tomorrow."

"Fine." Kaidan growls then storms out of the office.

Kaidan goes home and changes into civilian clothes then goes to Stanley Park hoping a walk would help him clear his head. The walk turned into a jog then into a full blown run as the thought of someone abusing Shepards memory makes his blood boil, Shepard sacrificed too much for someone to spoil his name. Needing a drink Kaidan goes to closest bar he can find.

Kaidan is still angry when he gets back homes smelling of the bar he was at, so he grabs his bottle of whiskey and a glass and quickly downs a few drinks hoping to calm his nerves. After the fourth shot of whiskey he looks down at his glass and notices his wedding ring still on his hand, with an angry yell he throws his cup against the wall shattering it into a thousand pieces then violently pulls the ring from his finger and tosses it. He grabs his bottle and drops down on his couch chugging the amber liquid planning on drowning all thought from his head. When the bottle is empty Kaidan tries to get up so he can find another but stumbles and falls, he opens his eyes and finds his wedding ring in front of his face its inscription clearly visible. Kaidan cries out and grabs it, slipping it back on his finger while tears roll down his cheeks. Crying he drags himself to bed, maybe it really is Shepard crosses his mind as he passes out.


	4. Freeing a Legend

Kaidan wakes up to his head throbbing, he pops some aspirin and has a shower to wash away the scent of liquor then dresses and quickly leaves. He gets a message from Hackett while he is getting into his skycar. Kaidan makes it to the Alliance HQ in record time, hoping and fearing what has been discovered about the assailant. He meets up with Hackett at his office.

"Sit down." Hackett says gesturing to the chair in front of his desk.

Kaidan sits down then Hackett pushes a datapad towards him. "What am I looking at?" Kaidan asks while activating the pad and shifting through results.

"We ran blood tests, DNA tests and every other test we could think of and all results came back positive but that could prove that he is a clone so we did a full body scan." Hackett says while reaching over and scrolling down to the scan results.

Kaidan reads it, his eyes go wide. "He has implants?" Kaidan asks a little shocked.

"I sent the results to Dr. Chakwas since she treated Shepard the most after Cerberus rebuilt him and she confirmed that they are accurate. This is what convinced me though." Hackett replies then scrolls the datapad down to a brain scan.

The scan shows a chip embedded deep in the brain, the blood drains from Kaidans face. "Is that a control chip?" He asks shakily.

"We believe so. He is in surgery as we speak, the doctors are attempting to remove it." Hackett says.

"How? I buried him two years ago. I held his body in my arms." Kaidan says getting worked up.

"You said it yourself yesterday. Cerberus cloned Shepard before they can do it again. They must have left a clones body to stop any search for him, we only did a DNA test to confirm the body's ID. The question now is why. Shepard is one of the best infiltrators in the galaxy but this is rather extensive for an assassin and with his free will stripped by a control chip his leadership skills are useless." Hackett states.

"So you think it's really him?" Kaidan asks.

"I want to question him still but yes, I do think it could be Shepard." Hackett replies.

Kaidan goes silent and glares at the control chip in the scan, the reason why he lost two years with John...again. He is going to find Cerberus or whatever group is responsible and make them pay for stealing his husband. I need to get ahold of Liara she might be able to point me in the right direction Kaidan thinks.

"I need to call some of my contacts. Do you mind if I take this?" Kaidan asks holding up the datapad.

"Of course, I'll message you when Shepard is out of surgery." Hackett answers.

"Thanks." Kaidan replies then hurries out.

Kaidan calls Liara on his way to his skycar. "Hey Liara are you still on earth?" He asks when she answers.

"I am for a couple more hours but..." She replies.

"Good. We need to talk." Kaidan says cutting her off.

"Kaidan I'm really busy right now can this wait?" Liara asks.

"It's about Shepard." He replies.

"Ok I will meet you at your apartment." She says after a brief pause.

"Thanks Liara." Kaidan replies then ends the call and heads home.

Kaidan is home for a few minutes before Liara shows up. He gestures towards his couch and sits down. Liara follows him and sits down as well.

"What is going on Kaidan?" Liara asks.

"Two nights ago the human councillor was assassinated. My investigation hinted at Cerberus or at least a like minded organization. After finding two more similar cases I had a meeting with Hackett. We were attacked by a masked assailant and were just barely able to subdue him. It was John." Kaidan explains.

"Are you sure?" Liara asks.

Kaidan hands her the datapad and she quickly starts looking at the test results. "It looks like it might be. The Alliance wants to interrogate him but the physical evidence is pretty damn convincing. He is in surgery right now so they can remove the control chip." He says.

"I knew something was going on. Everything was too quiet." Liara says getting up to leave. "I'll get my agents to look into this. Keep me informed on Shepard."

"I will." Kaidan replies walking her to the door.

Half an hour later Kaidan recieves a message informing him that the surgery was a success. Truly smiling for the first time in two years Kaidan leaves his home and goes back to Alliance HQ where his husband is waiting for him.

 

                                                                                  ***

John opens his eyes and groans at the throbbing in his head, he sits up slowly and holds his head feeling bandages wrapped around it. Confused he looks around noting the sterile white room with medical equipment and the flimsy hospital gown he has on. His attention is drawn to the door when a nurse walks in and let's out a squeak and hurries back out when she sees that he is awake.

After about ten minutes Admiral Hackett enters the room. "Admiral. What's going on? Are the reapers destroyed?" John asks.

"The reapers? Yes they were." Hackett answers sounding confused. "Shepard what is the last thing that you remember?"

John thinks for a minute, his memories are a bit fuzzy like trying to remember a vague dream. "I remember firing the crucible then there was an explosion, after that it's just flashes of faces and hospital rooms." He answers.

"It's been two years since the defeat of the reapers, the Normandy crew recovered what was believed to be your body. We now suspect the body was a clone and you have been with Cerberus the entire time." Hackett explains.

"Two years. Again." John exclaims then starts trying to get up. "Where is Kaidan, I need to see him."

Hackett stops him. "Calm down Shepard, you just came out of surgery. Kaidan will be hear shortly." He says.

"What surgery?" John asks remembering the bandages on his head.

"We had to remove a control chip implanted in your brain." Hackett answers.

"Control chip? What did they make me do?" Shepard asks seriously.

"They were using you as an assassin. You killed several political figures including the human councillor. You need to understand Shepard, we don't blame you. It's obvious that you weren't control of yourself." Hackett explains.

Shepard turns away angrily. "A councillor. I'm a spectre I'm suppose to protect them." John growls out.

Just then the door opens and the one person John wants to see walks in. Kaidan has more grey and deeper lines around his eyes but he still takes Johns breath away. He looks at John sternly but John can tell he is struggling to hold his emotions in.

"Admiral. I need to talk to... Shepard alone." Kaidan requests.

"Of course Alenko." Hackett says then nods at John before leaving. John can tell there will be more questions but right now he only cares about Kaidan.

Kaidan walks over to window and stares outside with his hands behind his back. John goes to say something but Kaidan holds up a hand silencing him. "I just need to know one thing. What is your name?" Kaidan asks without turning and facing him.

"John Alenko. We got married during shore leave before attacking Cerberus. I took your name in the hopes that after we could live a normal life." John says quietly. "You proposed but I convinced you to get married that night."

John watches as Kaidan begins to shake slightly then a slight sound comes from the man and he realizes Kaidan is crying. Ignoring the pain in his head John stands up and goes and takes Kaidan in his arms.

"Shhhh. It's gonna be alright Kaidan." John whispers into Kaidans ear comforting him.

"It's really you John." Kaidan whispers.

"Yeah it is." John replies.

Kaidan reaches up and gently pulls John into a chaste kiss but he can feel the desperation behind it. It's then John realized that believing he was dead almost killed Kaidan and Cerberus is responsible again. There is only one response to that, no one hurts the people he cares about and lives.


	5. Sex and Revelations

**Notes for the Chapter:**

> Warning this chapter has sex and mention of attempted suicide.

Kaidan hands John a red shirt, grey hoodie and some black jeans to change into, he can't help but watch him pull the clothes on admiring the muscular body of his husband. After two weeks of tests and questions Kaidan is finally allowed to take John home. His omni-tool beeps with a message from Liara saying she found a possible Cerberus lab and is sending agents in for recon.

"Finally." Kaidan exclaims, Cerberus locations have been even more well hidden than before.

John comes up behind Kaidan and wraps his arms around him. "Liara find something?" He asks.

"Maybe, she is doing recon and will contact us later." Kaidan says then gasps as John begins kissing his neck.

"Good. I can't wait to get home with you." John whispers huskily in between kisses then gently brushes his tongue against Kaidans amp port sending a shiver of pleasure down his body.

"Fuck stop John." Kaidan says feeling blood rush to his groin. "Let's get home first."

Kaidan pulls away but turn around and kisses John passionately before going and opening the door. He smirks when he sees John adjust his pants slightly before leaving the room. Kaidan pulls John hood up as they walk through the building, the Alliance wants to keep John's survival quiet for now and they are hoping to keep it that way. They make it to the skycar with no incident and Kaidan quickly sets it on the shortest route to his no their apartment.

"What are you thinking about?" John asks.

"Huh?" Kaidan says drawn out of his thoughts.

"You have this cute little smile." John replies.

Kaidan smiles even more. "Just thinking about how happy I am." He says happily.

John just smiles that rare all out smile few ever see, Kaidan reaches out and takes John's hand in his laces their fingers together then moves John's hand to his lips and places a gentle kiss, a sappy gesture but it feels right. The rest of the ride was silent, they just smile and hold hands. At their building Kaidan parks the skycar, they go inside and take the elevator.

Once the elevator doors close John pins Kaidan against the wall and begins kissing and nibbling on his neck while a firm leg is pushed between his own. Moaning Kaidan pulls John into a bruising kiss while grinding his growing erection into his husbands leg. The elevator dings and the door opens at their floor, they tumble through not wanting to stop kissing and struggle to the door that thankfully opens when the lock recognizes Kaidans omni-tool. In the apartment he takes control guiding John to the room, leaving a seductive trail of their clothing on the way.

Down to their briefs Kaidan pushes John back onto the bed and stands back admiring a view he thought he would never see again. He slowly pulls down his briefs and hears his husband suck in a breath when his cock bobs free. Kaidan climbs on top then kisses John, he traces the seam of his lips gaining entrance which he take advantage of and thoroughly plunders his mouth. Gasping for breath John grabs Kaidans ass and begins thrusting up, Kaidan moans at the rough feel of John's briefs against his bare cock but wants more and starts pulling at them.

"Just a sec." John says then starts trying to wiggles his briefs off so Kaidan lifts himself up to give him room but starts playing with his nipples making John moan.

"That's better." John says huskily while tossing his brief aside. "Now come here."

John pulls Kaidan back down and they both gasp as their cocks rub against each other. Kaidan thrusts his hips against John, getting a good rhythm going when he feels John's fingers brush against his amp port making him cry out in pleasure. He reaches down and starts stroking their cocks together as John puts a finger in his mouth which he sucks on greedily slicking it up.

John's finger pushes into his ass and starts fucking him. "Fuck John! It's been so long." Kaidan cries out. 

"Kai I want you to ride me." John says lustfully as he pushes a second finger into Kaidan stretching him and making him release their cocks as he is overwhelmed.

"Yeah." Kaidan struggles to say with John's fingers sliding deeper. "I... Mmm... I have lube in the end table drawer."

Kaidan whimpers when John removes his fingers so he can get the lube, leaving him feeling empty but the thought of John's cock inside him makes his arousal twitch with excitement. When John pulls out the bottle he raises an eyebrow to Kaidan as he unwraps the packaging but is soon more concerned with lubing himself up. Kaidan lifts himself up while John positions his cock. He slides down moaning when he feels the blunt pressure of John's cock pushing into him. Kaidan winces but controls the pain as he slides down forcing John in fully, he pauses for a bit while John's hands roam all over his body. When he's ready Kaidan sits up and places his hands on John's chest then locks eyes with him, he watches his Adam's apple bob with anticipation. Kaidan lifts himself almost all the way up before slamming back down drawing a load moan from them both. He starts riding John like he was born to hitting the perfect angle as if it was just yesterday when they last fucked. The room is filled with their gasps and moans but Kaidan couldn't care because it's been so long since he felt this.

John's hands run down Kaidans back. "Yeah Kai like that. God your so fucking beautiful like this." John moans out.

Kaidans rhythm falters slightly when John grabs his cock and starts stroking him hard. "Fuck John, I'm going to cum." Kaidan gasps out feeling his climax build faster than he expected.

"Do it Kaidan, cum around my cock." John says then reaches up and rubs his hand against Kaidan amp port.

The stimulation is too much making Kaidans biotic field snap around them as he cries out, his orgasm ripping through his body making him clench around John's cock. Kaidans vision blacks out but he feels John grip his hips and thrust up several more times before calling out Kaidans name as his cook pulses filling him with hot cum. He collapses on top of John both of them breathing heavily, they share a kiss before Kaidan rolls himself over and gets up, he goes to adjoining washroom and grabs a cloth wetting it down so they can clean up. Kaidan slowly wipes John's chest clean then tosses the cloth aside as John pulls him back to the bed to spoon with him. 

John kisses Kaidans shoulders and holds onto him tightly just like two years ago. "I love you." He whispers.

Kaidan smiles the emptiness inside finally dissipating. "I love you to." He replies.

John's hands wander across Kaidans body and he starts to think round two might be in order when John's fingers brush across his tags and lifts them to see. "Have you been wearing these the whole time?" He asks holding the dull and scorched set with John's name printed on them.

"Mostly." Kaidan says quietly the emotions hinting in his voice. "The first couple months were the hardest."

"I'm sorry Kaidan." John replies sadly. "Do you want to talk about it."

Kaidan sits up and rests his head in his hands. "After I left the Normandy I went to my family's orchard to look for my mother but it had been destroyed and my mother, she was gone. I started drinking and trying to pick fights hoping someone would kill me but most just avoided me either knowing who I was or seeing that I didn't give two shits if I lived or died. The Alliance ended up placing me on leave and relieving me of my weapons due to my mental state." He says then stands up and begins pacing. "You have to understand John, I was in a bad place. I had lost everything."

John stands ups and grabs Kaidan by the shoulder stopping his pacing. "What did you do Kaidan?" John said and Kaidan can see fear in his eyes.

"I...uh...I tried to kill myself. Liara found me in the bathtub with my wrists slashed, she barely got me to the hospital in time. While I was recovering she melded minds with me and showed me your memories of me and they were beautiful no even that doesn't describe them but they made me realize that you didn't save the galaxy for everyone but that you saved it for me and killing myself was just spitting on that. After my recovery I went back to the Alliance and immersed myself in work, once the council got back on their feet I started taking spectre missions as well. I felt that if I could help people then I was doing something worthwhile with my life." Kaidan goes silent waiting for John to say something.

Strong arms wrap around Kaidans waist and pulls him close. "I'm sorry. I don't know why Cerberus took me but I promise you we will make them pay." John says but Kaidan can hear anger in his voice.

Kaidan turns around and kisses John. "Come on let's make something to eat then maybe have a shower." Kaidan says trying to change the mood.

John get his mischievous look. "Only if you will fuck me in the shower." He says grabbing Kaidans ass.

"You read my mind." Kaidan replies happily.


	6. Memories

**Notes for the Chapter:**

> I'm sorry it took so long for this chapter my life had went crazy but should be back on track.

_"Mr. Shepard you know what happens when you disobey." The doctor says._

_"Fuck you." John yells out refusing to move._

_The doctor sighs then presses a few buttons on his omni-tool. Pain races through John's body it feels as though his very nerves are on fire, then he feels himself stand up and pick a pistol up from a table. Before he knows it the weapon is loaded and he is shooting an innocent woman tied to a chair._

John wakes up breathing heavily and eyes racing around the dark room as recognition slowly sinks in, he gently moves his husbands arm from around his waist and stands up. He quietly makes his way to the washroom closing the door behind him before turning on the sink and splashing some water on his face. John looks in the mirror glaring at his reflection, beads of water drip down his face yet he can remember when it was blood he unwillingly spilt.

"John!" Kaidan calls out.

John turns his head to the door, his heart clenching at the desperate sound of Kaidans voice. "In here." John calls back.

Kaidan opens the door and John can see fear still etched on his face. "Are you ok?" Kaidan asks.

"Yeah, just a bad memory." John replies then sighs. "There was a women they made me kill. It makes me wonder how many I killed for them."

"That wasn't you John. You don't blame the weapon you blame the one wielding it." Kaidan says then turns Johns face to look at him. "Maybe not the best comparison but it's true everything you did is Cerberus's fault not yours."

"I know, it's just... hard." John replies. "The last time I felt so helpless was when I was a child struggling to live on the streets."

"I know, but you are not helpless now and when we find Cerberus we will make them pay. Come on let's go back to bed, it's still early." Kaidan says then leaves the washroom.

John sighs quietly but follows Kaidan. They snuggle up in bed and Kaidan wraps his arms around John. It's doesn't take long before Kaidans breath evens out as he falls back to sleep but John lays there wide awake. He needs to figure out who that doctor is, John knows he is important somehow.

When sunlight starts to shine through the curtains John gets up again, this time he quietly pulls on some pants and leaves the room going to the kitchen so he can make breakfast for Kaidan. Before too long John has some bacon frying and a bowl full of pancake batter just waiting for the griddle to heat up, half and hour later he has two plates pilled high with fluffy golden pancakes and crisp bacon. While rummaging around in the cupboards looking for a tray he hears the sound of footsteps behind him.

"This was suppose to be breakfast in bed." John says while turning around and taking in the sight of his husband standing there with nothing on but a pair of sweatpants.

Kaidan smiles and goes up to the plates to snag a piece of bacon. "It smelled too good to wait, plus I burned a lot of calories yesterday." He says jokingly.

"Go sit at the table and I will pour you some coffee." John says chuckling slightly.

Kaidan sits down and John places a plate and some maple syrup in front of him before going to the coffee maker to pour two steaming cups. He adds cream and sugar being generous with Kaidans before placing the mugs on the table. Sitting down John smiles as he takes a sip of coffee while he watches his husband pour enough syrup to drown his pancakes.

"Do you want some pancakes with your syrup?" John asks teasingly.

"Hey it's maple syrup." Kaidan replies as if that explains everything.

John shakes his head slightly and grabs the peanut butter. "You're such a Canadian." He says lovingly.

"Well it's a heck of a lot better then your peanut butter and jam." Kaidan counters.

"Hey no one disses PB and J." John says emphasizing his point with a butter knife covered with peanut butter. "It's the perfect combination."

They both look at each other then laugh at the ridiculousness of their debate. "I love you Kaidan, don't ever change." John says smiling.

"I love you to." Kaidan replies.

They had barely started eating when Kaidans omni-tool beeped with an incoming call. He activates the vid screen bringing up Liara's face. "Hey Liara did you find anything?" Kaidan asks.

"Good morning you two." Liara replies then gets more serious. "Well when my team infiltrated the base it was abandoned, they did managed to download some corrupted data that I have experts working on right now. We do know that this was definitely a Cerberus base and we have a name. Doctor Jordan Bernfield."

The name catches John's attention as memories start to flood his mind.

_John slowly opens his eyes only to be blinded by a bright light, he goes to cover his eyes with his hand only to find he is restrained._

_"Good you're awake Mr. Shepard." A male voice says._

_"Who are you? What's going on?" John yells._

_"We are running a test. Now will you please blink your left eye." The man asks._

_"Fuck you." John says then pain shoots through his head, blackening his vision as agony courses through his skull, when it stops he finds his left eye blinking against his will. "What the hell?"_

_"Excellent. Now the right one." The man asks._

_Again John refuses and again he is wracked with pain then his right eye blinks on its own._

_"Excellent, you are progressing much faster then we." The man pauses as the sound of footsteps come close._

_"Excuse me Doctor Bernfield you have an urgent message." A woman says._

_"I'm sorry Mr. Shepard we will have to continue this later." Bernfield says then John starts to feel woozy as some drug is injected into him._

John shakes his head clearing the memory from his mind. "I believe this Bernfield was the doctor in charge. I remember him." He says.

"I have my best people looking into it." Liara replies.

"Thanks Liara." Both John and Kaidan say before ending the call.

Kaidan looks over at John. "So this doctor, is he the one who?" He asks.

"Yes." John replies. "Almost every memory I have he is there telling me what to do."

John looks down at his partially eaten pancakes but his appetite is gone so he pushes the plate away and gets up. "I'm going to take a shower." He says then heads to the washroom.

"Alright, I'll be there in a bit." Kaidan replies before taking another bite of his breakfast.

In the washroom John quickly undresses and sets the shower to almost pure hot before climbing in. He grits his teeth at the scalding water as he moves his head under the spray hoping to wash away the feel of his skin crawling.

_"Good morning Shepard." Dr. Bernfield says._

_"Doctor." John replies without emotion._

_"Mr. Manning has a new assignment for you." Dr. Bernfield says handing a datapad to John._

_He quickly scans through the file taking in names and locations before setting it down and going to his locker to suit up. "I will need a transport." John says._

_"There is one in the hanger, it will be under the guise of a material shipment." Dr. Bernfield replies._

_"Good." John says monotonously while strapping a sword to his back and pulling on his mask._

John is pulled back to reality when Kaidan places his hand on his shoulder. He looks at Kaidan with a devestated look in his eyes.

"I stopped fighting." He whispers.

Kaidan turns the shower off and pulls John into his arms. "Everyone breaks eventually John. You are only human." Kaidan replies.

"I almost killed you Kaidan." John remarks.

"But you didn't. That shows how strong you really are." Kaidan says.

Kaidans words hit him because he is right. When it really mattered he managed to break free long enough for them to stop him, not much difference to Benezia on Novaria, only when they deal with Cerberus Kaidan and him can finally live at peace.


End file.
